bool CSteadyStateTask::initialize(const OutputFlag & of,
COutputHandler * pOutputHandler,
std::ostream * pOstream)
{
bool success = true;
assert(mpProblem && mpMethod);
CSteadyStateProblem* pProblem =
dynamic_cast<CSteadyStateProblem *>(mpProblem);
assert(pProblem);
success &= pProblem->initialize();
CSteadyStateMethod* pMethod =
dynamic_cast<CSteadyStateMethod *>(mpMethod);
assert(pMethod);
success &= pMethod->initialize(pProblem);
success &= pMethod->isValidProblem(mpProblem);
success &= updateMatrices();
mSteadyState = mpContainer->getState(true);
success &= CCopasiTask::initialize(of, pOutputHandler, pOstream);
return success;
}
bool CSteadyStateTask::process(const bool & useInitialValues)
{
if (useInitialValues)
{
mpProblem->getModel()->applyInitialValues();
}
*mpSteadyState = mpProblem->getModel()->getState();
// A steady-state makes only sense in an autonomous model,
// i.e., the time of the steady-state must not be changed
// during simulation.
C_FLOAT64 InitialTime = mpSteadyState->getTime();
CSteadyStateMethod* pMethod =
dynamic_cast<CSteadyStateMethod *>(mpMethod);
assert(pMethod);
CSteadyStateProblem* pProblem =
dynamic_cast<CSteadyStateProblem *>(mpProblem);
assert(pMethod);
output(COutputInterface::BEFORE);
//call the method
mResult = pMethod->process(mpSteadyState,
mJacobianX,
mpCallBack);
if (mResult == CSteadyStateMethod::notFound)
restore();
//update jacobian
if (pProblem->isJacobianRequested() ||
pProblem->isStabilityAnalysisRequested())
{
pMethod->doJacobian(mJacobian, mJacobianX);
}
//mpProblem->getModel()->setState(mpSteadyState);
//mpProblem->getModel()->updateRates();
//calculate eigenvalues
if (pProblem->isStabilityAnalysisRequested())
{
mEigenValues.calcEigenValues(mJacobian);
mEigenValuesX.calcEigenValues(mJacobianX);
mEigenValues.stabilityAnalysis(pMethod->getStabilityResolution());
mEigenValuesX.stabilityAnalysis(pMethod->getStabilityResolution());
}
// Reset the time.
mpSteadyState->setTime(InitialTime);
C_FLOAT64 * pTo;
size_t i;
// construct Eigenvalues of Jacobian
CVector< C_FLOAT64 > vectorEigen_R = mEigenValues.getR();
CVector< C_FLOAT64 > vectorEigen_I = mEigenValues.getI();
#ifdef DEBUG_UI
C_INT32 size = vectorEigen_R.size() + vectorEigen_I.size();
std::cout << "vectorEigen_R.size() = " << vectorEigen_R.size() << " + vectorEigen_I.size() = " << vectorEigen_I.size() << " == " << size << std::endl;
std::cout << "size = " << mEigenvaluesXMatrix.size() << std::endl;
#endif
assert(vectorEigen_R.size() == vectorEigen_I.size());
pTo = mEigenvaluesMatrix.array();
for (i = 0; i < vectorEigen_R.size(); ++i)
{
*pTo = vectorEigen_R[i]; ++pTo;
*pTo = vectorEigen_I[i]; ++pTo;
}
#ifdef DEBUG_UI
std::cout << mEigenvaluesMatrix << std::endl;
#endif
// construct Eigenvalues of Jacobian of reduced system
CVector< C_FLOAT64 > vectorEigenX_R = mEigenValuesX.getR();
CVector< C_FLOAT64 > vectorEigenX_I = mEigenValuesX.getI();
#ifdef DEBUG_UI
C_INT32 sizeX = vectorEigenX_R.size() + vectorEigenX_I.size();
std::cout << "vectorEigenX_R.size() = " << vectorEigenX_R.size() << " + vectorEigenX_I.size() = " << vectorEigenX_I.size() << " == " << sizeX << std::endl;
std::cout << "size = " << mEigenvaluesXMatrix.size() << std::endl;
#endif
assert(vectorEigenX_R.size() == vectorEigenX_I.size());
pTo = mEigenvaluesXMatrix.array();
for (i = 0; i < vectorEigenX_R.size(); ++i)
{
*pTo = vectorEigenX_R[i]; ++pTo;
*pTo = vectorEigenX_I[i]; ++pTo;
}
#ifdef DEBUG_UI
std::cout << mEigenvaluesXMatrix << std::endl;
#endif
output(COutputInterface::AFTER);
return (mResult != CSteadyStateMethod::notFound);
}
bool CSteadyStateTask::initialize(const OutputFlag & of,
COutputHandler * pOutputHandler,
std::ostream * pOstream)
{
assert(mpProblem && mpMethod);
if (!mpMethod->isValidProblem(mpProblem)) return false;
bool success = true;
if (!updateMatrices())
return false;
success &= CCopasiTask::initialize(of, pOutputHandler, pOstream);
pdelete(mpSteadyState);
mpSteadyState = new CState(mpProblem->getModel()->getInitialState());
mCalculateReducedSystem = (mpProblem->getModel()->getNumDependentReactionMetabs() != 0);
#ifdef xxxx
// init Jacobians
size_t sizeX = mpSteadyState->getNumIndependent();
mJacobianX.resize(sizeX, sizeX);
size_t size = sizeX + mpSteadyState->getNumDependent();
mJacobian.resize(size, size);
//jacobian annotations
CStateTemplate & StateTemplate = mpProblem->getModel()->getStateTemplate();
mpJacobianAnn->resize();
CModelEntity **ppEntities = StateTemplate.getEntities();
const size_t * pUserOrder = StateTemplate.getUserOrder().array();
const size_t * pUserOrderEnd = pUserOrder + StateTemplate.getUserOrder().size();
pUserOrder++; // We skip the time which is the first.
size_t i, imax = size;
for (i = 0; i < imax && pUserOrder != pUserOrderEnd; pUserOrder++)
{
const CModelEntity::Status & Status = ppEntities[*pUserOrder]->getStatus();
if (Status == CModelEntity::ODE ||
(Status == CModelEntity::REACTIONS && ppEntities[*pUserOrder]->isUsed()))
{
mpJacobianAnn->setAnnotationCN(0 , i, ppEntities[*pUserOrder]->getCN());
mpJacobianAnn->setAnnotationCN(1 , i, ppEntities[*pUserOrder]->getCN());
i++;
}
}
mpJacobianXAnn->resize();
ppEntities = StateTemplate.beginIndependent();
imax = sizeX;
for (i = 0; i < imax; ++i, ++ppEntities)
{
mpJacobianXAnn->setAnnotationCN(0 , i, (*ppEntities)->getCN());
mpJacobianXAnn->setAnnotationCN(1 , i, (*ppEntities)->getCN());
}
#endif
CSteadyStateProblem* pProblem =
dynamic_cast<CSteadyStateProblem *>(mpProblem);
assert(pProblem);
success &= pProblem->initialize();
CSteadyStateMethod* pMethod =
dynamic_cast<CSteadyStateMethod *>(mpMethod);
assert(pMethod);
success &= pMethod->initialize(pProblem);
return success;
}